Job ID = 16438087 SRX = SRX10031701 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32895047 spots for SRR13634471/SRR13634471.sra Written 32895047 spots for SRR13634471/SRR13634471.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438423 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:05 32895047 reads; of these: 32895047 (100.00%) were unpaired; of these: 2060966 (6.27%) aligned 0 times 25802657 (78.44%) aligned exactly 1 time 5031424 (15.30%) aligned >1 times 93.73% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 9626271 / 30834081 = 0.3122 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 13:53:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:53:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:53:58: 1000000 INFO @ Tue, 02 Aug 2022 13:54:05: 2000000 INFO @ Tue, 02 Aug 2022 13:54:11: 3000000 INFO @ Tue, 02 Aug 2022 13:54:17: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 13:54:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:54:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:54:24: 5000000 INFO @ Tue, 02 Aug 2022 13:54:27: 1000000 INFO @ Tue, 02 Aug 2022 13:54:30: 6000000 INFO @ Tue, 02 Aug 2022 13:54:32: 2000000 INFO @ Tue, 02 Aug 2022 13:54:36: 7000000 INFO @ Tue, 02 Aug 2022 13:54:38: 3000000 INFO @ Tue, 02 Aug 2022 13:54:43: 8000000 INFO @ Tue, 02 Aug 2022 13:54:43: 4000000 INFO @ Tue, 02 Aug 2022 13:54:49: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:54:49: 9000000 INFO @ Tue, 02 Aug 2022 13:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 13:54:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:54:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:54:54: 6000000 INFO @ Tue, 02 Aug 2022 13:54:56: 10000000 INFO @ Tue, 02 Aug 2022 13:54:57: 1000000 INFO @ Tue, 02 Aug 2022 13:55:00: 7000000 INFO @ Tue, 02 Aug 2022 13:55:02: 11000000 INFO @ Tue, 02 Aug 2022 13:55:03: 2000000 INFO @ Tue, 02 Aug 2022 13:55:05: 8000000 INFO @ Tue, 02 Aug 2022 13:55:08: 12000000 INFO @ Tue, 02 Aug 2022 13:55:09: 3000000 INFO @ Tue, 02 Aug 2022 13:55:11: 9000000 INFO @ Tue, 02 Aug 2022 13:55:15: 4000000 INFO @ Tue, 02 Aug 2022 13:55:15: 13000000 INFO @ Tue, 02 Aug 2022 13:55:16: 10000000 INFO @ Tue, 02 Aug 2022 13:55:20: 5000000 INFO @ Tue, 02 Aug 2022 13:55:21: 14000000 INFO @ Tue, 02 Aug 2022 13:55:21: 11000000 INFO @ Tue, 02 Aug 2022 13:55:26: 6000000 INFO @ Tue, 02 Aug 2022 13:55:27: 12000000 INFO @ Tue, 02 Aug 2022 13:55:28: 15000000 INFO @ Tue, 02 Aug 2022 13:55:31: 7000000 INFO @ Tue, 02 Aug 2022 13:55:32: 13000000 INFO @ Tue, 02 Aug 2022 13:55:34: 16000000 INFO @ Tue, 02 Aug 2022 13:55:37: 8000000 INFO @ Tue, 02 Aug 2022 13:55:38: 14000000 INFO @ Tue, 02 Aug 2022 13:55:40: 17000000 INFO @ Tue, 02 Aug 2022 13:55:42: 9000000 INFO @ Tue, 02 Aug 2022 13:55:43: 15000000 INFO @ Tue, 02 Aug 2022 13:55:47: 18000000 INFO @ Tue, 02 Aug 2022 13:55:47: 10000000 INFO @ Tue, 02 Aug 2022 13:55:49: 16000000 INFO @ Tue, 02 Aug 2022 13:55:53: 11000000 INFO @ Tue, 02 Aug 2022 13:55:53: 19000000 INFO @ Tue, 02 Aug 2022 13:55:54: 17000000 INFO @ Tue, 02 Aug 2022 13:55:58: 12000000 INFO @ Tue, 02 Aug 2022 13:55:59: 20000000 INFO @ Tue, 02 Aug 2022 13:56:00: 18000000 INFO @ Tue, 02 Aug 2022 13:56:04: 13000000 INFO @ Tue, 02 Aug 2022 13:56:05: 19000000 INFO @ Tue, 02 Aug 2022 13:56:06: 21000000 INFO @ Tue, 02 Aug 2022 13:56:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:56:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:56:07: #1 total tags in treatment: 21207810 INFO @ Tue, 02 Aug 2022 13:56:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:56:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:56:07: #1 tags after filtering in treatment: 21207810 INFO @ Tue, 02 Aug 2022 13:56:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:56:07: #1 finished! INFO @ Tue, 02 Aug 2022 13:56:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:56:09: #2 number of paired peaks: 834 WARNING @ Tue, 02 Aug 2022 13:56:09: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Tue, 02 Aug 2022 13:56:09: start model_add_line... INFO @ Tue, 02 Aug 2022 13:56:09: start X-correlation... INFO @ Tue, 02 Aug 2022 13:56:09: 14000000 INFO @ Tue, 02 Aug 2022 13:56:09: end of X-cor INFO @ Tue, 02 Aug 2022 13:56:09: #2 finished! INFO @ Tue, 02 Aug 2022 13:56:09: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 13:56:09: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 13:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.05_model.r INFO @ Tue, 02 Aug 2022 13:56:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:56:10: 20000000 INFO @ Tue, 02 Aug 2022 13:56:14: 15000000 INFO @ Tue, 02 Aug 2022 13:56:16: 21000000 INFO @ Tue, 02 Aug 2022 13:56:17: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:56:17: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:56:17: #1 total tags in treatment: 21207810 INFO @ Tue, 02 Aug 2022 13:56:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:56:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:56:17: #1 tags after filtering in treatment: 21207810 INFO @ Tue, 02 Aug 2022 13:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:56:17: #1 finished! INFO @ Tue, 02 Aug 2022 13:56:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:56:19: #2 number of paired peaks: 834 WARNING @ Tue, 02 Aug 2022 13:56:19: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Tue, 02 Aug 2022 13:56:19: start model_add_line... INFO @ Tue, 02 Aug 2022 13:56:19: start X-correlation... INFO @ Tue, 02 Aug 2022 13:56:19: end of X-cor INFO @ Tue, 02 Aug 2022 13:56:19: #2 finished! INFO @ Tue, 02 Aug 2022 13:56:19: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 13:56:19: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 13:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.10_model.r INFO @ Tue, 02 Aug 2022 13:56:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:56:20: 16000000 INFO @ Tue, 02 Aug 2022 13:56:25: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:56:30: 18000000 INFO @ Tue, 02 Aug 2022 13:56:35: 19000000 INFO @ Tue, 02 Aug 2022 13:56:40: 20000000 INFO @ Tue, 02 Aug 2022 13:56:45: 21000000 INFO @ Tue, 02 Aug 2022 13:56:46: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:56:46: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:56:46: #1 total tags in treatment: 21207810 INFO @ Tue, 02 Aug 2022 13:56:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:56:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:56:47: #1 tags after filtering in treatment: 21207810 INFO @ Tue, 02 Aug 2022 13:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:56:47: #1 finished! INFO @ Tue, 02 Aug 2022 13:56:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:56:48: #2 number of paired peaks: 834 WARNING @ Tue, 02 Aug 2022 13:56:48: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Tue, 02 Aug 2022 13:56:48: start model_add_line... INFO @ Tue, 02 Aug 2022 13:56:48: start X-correlation... INFO @ Tue, 02 Aug 2022 13:56:48: end of X-cor INFO @ Tue, 02 Aug 2022 13:56:48: #2 finished! INFO @ Tue, 02 Aug 2022 13:56:48: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 13:56:48: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 13:56:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.20_model.r INFO @ Tue, 02 Aug 2022 13:56:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:56:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:56:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:57:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.05_summits.bed INFO @ Tue, 02 Aug 2022 13:57:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10261 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.10_summits.bed INFO @ Tue, 02 Aug 2022 13:57:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7643 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:57:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031701/SRX10031701.20_summits.bed INFO @ Tue, 02 Aug 2022 13:57:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5115 records, 4 fields): 43 millis CompletedMACS2peakCalling